GeneticThesaurus is designed for analysis of genetic variation in repetitive regions. It contains programs that build a table describing genomic regions with similar sequence. It also provides tools that use the resource to annotate variants.
To run the GeneticThesaurus, you will need java (version 6 or above). Execute the program using the command
java -jar GeneticThesaurus.jar
You may need to provide the java virtual machine access to a larger pool of memory than is allowed by default. In such situations, additionally use the -Xmx flag. For example, to provide 24GB of heap memory, use
java -Xmx24g -jar GeneticThesaurus.jar
The project is developed on github.com and distributed on sourceforge.net under the name "GeneticThesaurus".
Usage information is available on the wiki pages at www.sourceforge.net.
GeneticThesaurus is described in an academic publication. If you find GeneticThesaurus useful, please cite
C. Kerzendorfer, T. Konopka, S. Nijman. "A thesaurus of genetic variation for interrogation of repetitive genomic regions" Nucleic Acids Research
T.Konopka, S. Nijman. "GeneticThesaurus: Comparison of matched samples with thesaurus annotation" (under review)
Source code is developed by Tomasz Konopka.
Copyright 2013-2015 Tomasz Konopka
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.